#29: update minimap2 and samtools versions; #27

mritchielab · Apr 8, 2024 · 842443d · 842443d
1 parent 2b84464
commit 842443d
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -87,7 +87,7 @@ Suggests:
     testthat (>= 3.0.0),
     xml2
 LinkingTo: Rcpp, Rhtslib, zlibbioc, testthat
-SystemRequirements: GNU make, C++17, samtools (>= 1.14), minimap2 (>= 2.28)
+SystemRequirements: GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17)
 RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 URL: https://github.com/OliverVoogd/FLAMES

diff --git a/R/minimap2_align.R b/R/minimap2_align.R
@@ -79,7 +79,9 @@ minimap2_align <- function(config, fa_file, fq_in, annot, outdir, minimap2 = NA,
         ">", file.path(outdir, "tmp_splice_anno.bed12")))
     if (!is.null(base::attr(paftoolsjs_status, "status")) && base::attr(paftoolsjs_status,
       "status") != 0) {
-      stop(paste0("error running k8 paftools.js gff2bed:\n", paftoolsjs_status))
+      stop(paste0("error running k8 paftools.js gff2bed:\n", paftoolsjs_status, "\n",
+        "Are you using NCBI GFF3? It is not well supported by minimap2's paftools.js"))
+      ))
     }
     minimap2_args <- base::append(minimap2_args, c("--junc-bed", file.path(outdir,
       "tmp_splice_anno.bed12"), "--junc-bonus", "1"))